FSL-MRS Voxel Location

jharoon · May 29, 2024, 11:09pm

Hi all!

We recently implemented a processing pipeline for processing .7 MRS files from a 3T GE scanner, specifically looking at SVS in the left-frontal region. However, for some reason, the ‘voxel location’ image displays the voxel as being on the right side / contralateral side of acquisition (this was confirmed by checking the original voxel placement done at the scanning center, which showed up on the left frontal region).

Curious if anyone else has run into the problem or has any suggestions on how to potentially resolve this - Thanks!

wclarke · May 30, 2024, 8:43pm

Hi @jharoon,

How do things look in fsleyes? If this is still wrong, it might be related to an issue I’m part way through fixing. See Conversion failure on GE data · Issue #123 · wtclarke/spec2nii · GitHub

jharoon · June 6, 2024, 9:42pm

Hi William,

Thanks for the quick response! I’m attaching a png of the voxel placement, post-processing in FSL_mrs. The voxel at acquisition was placed on the left side, but for all of our cases that we’ve processed, the FSL voxel placement seems to flip the orientation.

wclarke · June 7, 2024, 8:12am

Yes, I understand, but, as asked above, please load the data into fsleyes and see where the voxel is positioned. The fsleyes code is much more heavily validated, and therefore will indicate whether it is an issue with data conversion or the plotting code in FSL-MRS.

jharoon · June 7, 2024, 8:19pm

Ah understood, apologies! It looks like when the voxel nifti data is loaded into FSLeyes with the T1, it does appear on the correct side, but it is only after processing that it appears on the opposite side.

wclarke · June 9, 2024, 1:00pm

Thanks for checking. Could you run fslreorient2std on the T1 before passing it to the processing and then see whether that makes a difference for the case when it gets the wrong side?

jharoon · June 11, 2024, 8:47pm

Thanks for the suggestion! Unfortunately, tried it on two cases and that didn’t seem to work either

wclarke · June 26, 2024, 9:58am

Sorry, I let this slip as I’ve just got back from pat leave.

Is there any chance you could share the data, or even just the affine matricies from the T1 and the SVS data? (Run fslhd on each to get this)

jharoon · July 1, 2024, 9:22pm

Hi William,

No worries at all, and congratulations! I ran fslhd on both and I’m pasting the data for T1 and SVS below:

filename Anatomical/T1.nii.gz

sizeof_hdr 348

data_type INT16

dim0 3

dim1 372

dim2 512

dim3 324

dim4 1

dim5 1

dim6 1

dim7 1

vox_units mm

time_units s

datatype 4

nbyper 2

bitpix 16

pixdim0 1.000000

pixdim1 0.500000

pixdim2 0.500000

pixdim3 0.500000

pixdim4 2.390720

pixdim5 0.000000

pixdim6 0.000000

pixdim7 0.000000

vox_offset 352

cal_max 0.000000

cal_min 0.000000

scl_slope 1.000000

scl_inter 0.000000

phase_dim 0

freq_dim 0

slice_dim 0

slice_name Unknown

slice_code 0

slice_start 0

slice_end 0

slice_duration 0.000000

toffset 0.000000

intent Unknown

intent_code 0

intent_name

intent_p1 0.000000

intent_p2 0.000000

intent_p3 0.000000

qform_name Scanner Anat

qform_code 1

qto_xyz:1 0.499025 -0.031155 -0.001820 -87.371529

qto_xyz:2 0.031202 0.498644 0.019510 -51.212696

qto_xyz:3 0.000599 -0.019585 0.499616 -30.942078

qto_xyz:4 0.000000 0.000000 0.000000 1.000000

qform_xorient Left-to-Right

qform_yorient Posterior-to-Anterior

qform_zorient Inferior-to-Superior

sform_name Scanner Anat

sform_code 1

sto_xyz:1 0.499023 -0.031155 -0.001820 -87.371529

sto_xyz:2 0.031202 0.498644 0.019510 -51.212677

sto_xyz:3 0.000599 -0.019585 0.499616 -30.942078

sto_xyz:4 0.000000 0.000000 0.000000 1.000000

sform_xorient Left-to-Right

sform_yorient Posterior-to-Anterior

sform_zorient Inferior-to-Superior

file_type NIFTI-1+

file_code 1

descrip FSL5.0

filename MRS/proc/Frontal.nii.gz

sizeof_hdr 540

data_type COMPLEX64

dim0 6

dim1 1

dim2 1

dim3 1

dim4 4096

dim5 12

dim6 12

dim7 1

vox_units mm

time_units s

datatype 32

nbyper 8

bitpix 64

pixdim0 -1.000000

pixdim1 20.000000

pixdim2 20.000000

pixdim3 20.000000

pixdim4 0.000200

pixdim5 1.000000

pixdim6 1.000000

pixdim7 1.000000

vox_offset 1344

cal_max 0.000000

cal_min 0.000000

scl_slope 1.000000

scl_inter 0.000000

phase_dim 0

freq_dim 0

slice_dim 0

slice_name Unknown

slice_code 0

slice_start 0

slice_end 0

slice_duration 0.000000

toffset 0.000000

intent Unknown

intent_code 0

intent_name mrs_v0_8

intent_p1 0.000000

intent_p2 0.000000

intent_p3 0.000000

qform_name Aligned Anat

qform_code 2

qto_xyz:1 -20.000000 0.000000 -0.000000 -20.909908

qto_xyz:2 0.000000 -20.000000 -0.000000 117.590614

qto_xyz:3 0.000000 0.000000 -20.000000 66.839722

qto_xyz:4 0.000000 0.000000 0.000000 1.000000

qform_xorient Right-to-Left

qform_yorient Anterior-to-Posterior

qform_zorient Superior-to-Inferior

sform_name Aligned Anat

sform_code 2

sto_xyz:1 -20.000000 0.000000 0.000000 -20.909908

sto_xyz:2 0.000000 -20.000000 0.000000 117.590614

sto_xyz:3 0.000000 0.000000 -20.000000 66.839722

sto_xyz:4 0.000000 0.000000 0.000000 1.000000

sform_xorient Right-to-Left

sform_yorient Anterior-to-Posterior

sform_zorient Superior-to-Inferior

file_type NIFTI-2+

file_code 2